BACKGROUND: The application of transcranial direct current stimulation (tDCS) and repetitive transcranial magnetic stimulation (rTMS) in patients with early stroke has recently received considerable attention, but the optimal protocol remains inconclusive. This study intends to evaluate and compare the effects of different protocols of tDCS and rTMS on improving motor function, activities of daily living (ADL), and neurological function in patients with early stroke, and to comprehensively assess their efficacy and safety. METHODS: MEDLINE, Embase, Cochrane Library, and Web of Science were searched. Risk of bias (RoB) was assessed using the Cochrane Risk of Bias 2.0 tool, and Bayesian NMA was conducted using R4.3.1 and Stata16. RESULTS: The results of NMA showed that after early intervention, bilateral application of high- and low-frequency rTMS (BL-rTMS) performed best in improving the upper extremity motor function at the end of intervention (SUCRA: 92.8%) and 3 months (SUCRA: 95.4%). Besides, low-frequency rTMS (LF-rTMS) performed best in improving the lower extremity motor function (SUCRA: 67.7%). BL-rTMS was the most effective in ameliorating the ADL at the end of intervention (SUCRA: 100%) and 3 months (SUCRA: 85.6%). In terms of the NIHSS scores, BL-rTMS had the highest probability of being the most effective measure at the end of intervention (SUCRA: 99.7%) and 3 months (SUCRA: 97.05%). Besides, LF-rTMS (0%), 5 Hz-rTMS (0%), and intermittent theta-burst stimulation (iTBS) (0%) all exhibited a good safety profile. CONCLUSION: BL-rTMS is the optimal stimulation protocol for improving upper extremity motor function, ADL, and neurological function in early stroke, with long-term efficacy.